Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POU2F3

Cell type

Cell type Class
Lung
Cell type
COR-L311
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Small Cell

Attributes by original data submitter

Sample

source_name
small cell lung cancer tuft variant
cell line
CORL311
chip antibody
in house raised OCT11 Antibody
treatment
endogeneous

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was extracted using TRIzol following the standard protocol; cells were fixed with 1% formaldehyde for 10 minutes and quenched with glycine following standard protocol (see method in paper) for ChIP-Seq. polyA RNA was selected and fragmented with NEBNext Poly (A) mRNA Magnetic isolation module (NEB #E7350) and the library was prepared with NEBNext Ultra II RNA Library Prep kit for Illumina (NEB #E7770) with 2 ug RNA according to the manufacturer's protocol. For single cell RNA-seq, cell suspensions were stained for viability with Sytox blue (ThermoFisher S34857) and sorted on a Sony SH800S (Sony Biotechnology Inc, San Jose, CA) using a 100 μm chip (Catalog #LE-C3110) in “Ultra Purity” mode. Sorted cells were washed and resuspended in PBS containing 0.04% BSA. An aliquot was stained with ViaStain AOPI (Nexcelom #CS2-0106-5mL) and counted using a Countess FL II automated cell. Up to 12,000 cells were loaded per lane on 10X Chromium microfluidic chips. Single cell capture, barcoding, and library preparation were performed using the 10X Chromium chemistry, using the NextGEM Single-Cell 3' Library Kit v3.1 (1000121; 10X Genomics). ChIP-seq library was prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645) following manufacturer's protocol with AMPure XP beads (Beckman, A63881) with no size selection.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
53603504
Reads aligned (%)
98.2
Duplicates removed (%)
3.9
Number of peaks
14349 (qval < 1E-05)

hg19

Number of total reads
53603504
Reads aligned (%)
97.1
Duplicates removed (%)
5.2
Number of peaks
14092 (qval < 1E-05)

Base call quality data from DBCLS SRA